Hepatitis C virus is both difficult to treat and a significant cause of morbidity and mortality. To further understand the virological determinants of infection and the development of chronicity, the hepatitis C virus sequence in the early stages of infection has been determined from the same patients. In particular the sequencing effort is focused on the viral sequence before and after treatment, in the two patients who were HIV positive and relapsed. The complete sequence has been determined and is now being analyzed. A second laboraratory project has been to study the nature of late relapse after treatment for hepatitis C. The first 103 patients who achieved a sustained virologic response at the National Institutes of Health Clinical Center were reviewed (This has now been published). Three patients had a late relapse. The viral sequence from these patients was studied from before treatment, from the liver at the time of sustained virologic response, and from the serum at the time of documented relapse. The viral sequences obtained from before treatment, the liver at the time of sustained virologic response, and from the serum at the time of relapse were all virtually identical proving relapse and not reinfection. This manuscript is now published. A third laboratory project has been completed and used viral sequencing to understand discrepancies in commercial genotyping assays. This is now published. A second type of chronic hepatitis studied is hepatitis D. Hepatitis D is the most aggressive form of viral hepatitis as well as the most difficult to treat. Interferon therapy is the standard approach. Patients are typically treated for 6 months to a year. Relapse after cessation of therapy is the norm. In protocol 01-DK-0247 patients are treated with peginterferon for 5 years. The dose is titrated to maintain normal ALT and minimize side effects. Thirteen patients were enrolled, and of the 12 who have had one-year evaluations 10 have met the protocol definition of response. 3/13 patients (27%) lost HBsAg after 24, 37 and 202 weeks of treatment and developed HBs antibodies. Treatment was stopped in these patients at least 24 weeks later; the serological response was durable and was associated with persistent improvement of ALT and platelet count during follow-up. Two patients (15%) died during therapy, one from hepatocellular carcinoma and the other from herpes colitis. Both deaths were not considered related to treatment. There were no other serious adverse events and treatment was well-tolerated overall. 3 patients required a dose reduction due to cytopenias. The primary end point of the study is the evaluation after three years although it is planned to treat patients for 5 years. Hepatitis D viral RNA and hepatitis B surface antigen levels have been measured and the final analysis has been completed. This work is now published. In addition the viral kinetics noted during response are being analyzed. This work is now published. A second treatment trial for hepatitis D has been initiated with a prenylation inhibitor. Both phases of this study have been completed with 14 patients treated. The results are now published. The therapy was shown to have promise and to be safe when given for 28 days. A new project has been commenced looking at inflammatory markers and there association with liver disease progression in a cohort of patients with chronic hepatitis C.